User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.5k
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Italy
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@jotsetung
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Joined:
5 years, 1 month ago
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j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 278 results • page 1 of 28 • next >
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News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
... Dear all, I've added `ensembldb` `EnsDb` databases for all species of Ensembl release 98 to `AnnotationHub`. These databases provide now also the G-C nucleotide content for each transcript in metadata column `"gc_content"` (see below). cheers, jo ```r > library(AnnotationHub) > query(Annota ...
annotation annotationhub news ensembldb ensdb written 9 days ago by Johannes Rainer1.5k
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
... The Institute for Biomedicine is home to an international and interdisciplinary team of scientists, students and support staff, integrated in a network of international and national partners. Living and working in Bozen/Bolzano allows you to experience a unique combination of Alpine and Mediterranea ...
cancer job written 7 weeks ago by Johannes Rainer1.5k
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Could you please try to make a minimal example with the fewest files possible? you could send me an email to johannes.rainer at eurac.edu ...
written 8 weeks ago by Johannes Rainer1.5k
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Don't worry about the `x$.self$finalize()` calls - I did not find a way yet to get rid of them, but they don't affect the analysis. They occurr randomly. Now regarding the issue that you get, would it be possible for you to share the *BN_amide_092.mzXML* file and a second one of your files? It's ha ...
written 8 weeks ago by Johannes Rainer1.5k
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Dear Abbey, thank you for your detailed description of your issue! The error that you see comes from the *obiwarp* alignment. Without knowing your data it is now difficult to get to the exact cause, but I guess that obiwarp has a problem with the retention times in one file (e.g. because, as the er ...
written 11 weeks ago by Johannes Rainer1.5k
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Comment: C: xcms centwave roiList error
... Note that you can also provide a `matrix` with arguments `mz` and `rt` (two columns with lower and upper boundary, each row defining the region in wich you expect the data from one ion). With that you could extract multiple XIC at once and you could also run the `findChromPeaks` on all of them. That ...
written 4 months ago by Johannes Rainer1.5k
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Comment: C: xcms centwave roiList error
... The `findChromPeaks` function is really only intended to identify chromatographic peaks - not to extract ion chromatograms. To extract ion chromatograms you have to use the `chromatogram` function on the *on disk* data. It will extract the chromatogram for each file in your data. If you call `plot` ...
written 4 months ago by Johannes Rainer1.5k
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Answer: A: xcms centwave roiList error
... The `roiList` parameter should be a `list`. So what you should do is to provide the ROI as: ``` Trypto <- list(c(scmin = 51, scmax = 800, mzmin = 216.1321, mzmax = 216.1361, length = 20, intensity = 1000)) cwp <- CentWaveParam(roiList = Trypto) ``` Note however that it would be much easier t ...
written 4 months ago by Johannes Rainer1.5k
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Answer: A: Extracting Data from MSn experiment data ("OnDiskMSnExp")
... Hi James, the reason the `write.table` function takes so long is that in that call all processings are applied to the data. In the *on disk* mode all data manipulation operations are *cached* and only applied whenever you access the data (which in your case is when you call `write.table`, which in ...
written 4 months ago by Johannes Rainer1.5k
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Comment: C: XCMS - cannot allocate vector of size **Gb when global environment is empty
... Two things: 1) please change to the *new* functions/objects of `xcms` (see [xcms vignette](https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html)). 2) `profstep = 0.01` will create a huge matrix (which in your case will not fit into memory) - question is if you really nee ...
written 4 months ago by Johannes Rainer1.5k

Latest awards to Johannes Rainer

Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 10 months ago, created an answer that has been accepted. For A: Ensembl plants at annotationHub?
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve canonical transcript for each gene via ensembldb R package
Popular Question 13 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 13 months ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 13 months ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 14 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 15 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 18 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 18 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 2.4 years ago, received more than 100 upvotes.
Voter 2.4 years ago, voted more than 100 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 2.4 years ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 2.4 years ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Scholar 2.5 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 2.5 years ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function

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